研究者詳細 - 安永　卓生

その他リンク： https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85133102192&origin=inward

Extended supercomplex contains type-II NADH dehydrogenase, cytochrome bcc complex, and aa<inf>3</inf> oxidase in the respiratory chain of Corynebacterium glutamicum 査読有り国際誌

Takazaki H., Kusumoto T., Ishibashi W., Yasunaga T., Sakamoto J.

Journal of Bioscience and Bioengineering 133 ( 1 ) 76 - 82 2022年01月

記述言語：英語掲載種別：研究論文（学術雑誌）

To clarify the precise subunit composition of the respiratory supercomplex of Corynebacterium glutamicum, several wash conditions were examined. MEGA (9 + 10) wash-buffer (0.5%) was used for this purpose and two-step column chromatography was performed. Almost equal amounts of cytochrome c, b, and a were observed in the purified fraction, estimated by their different absorption spectra. The 833 kDa and 685 kDa bands were observed in the clear native polyacrylamide gel electrophoresis (CN-PAGE) of the purified fraction. Both bands were stained using N,N',N′,N-tetramethyl-p-phenylenediamine (TMPD) oxidase dye, and the 833 kDa band was also stained using NADH oxidase dye. The 3D map reconstructed from the 833 kDa band indicated that the bcc complex and aa3 oxidase are heterodimers. Lastly, electron transfer from NADH to the bcc-aa3 supercomplex was observed. The 833 kDa band is the supercomplex, which includes the heterodimer cytochrome bcc complex and cytochrome aa3 oxidase, as well as the monomer NDH-II. Hence, we termed the 833 kDa band the extended supercomplex (ESC).

DOI： 10.1016/j.jbiosc.2021.10.004

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Filopodia formation by crosslinking of F-actin with fascin in two different binding manners 査読有り国際誌

Shinji Aramaki, Kouta Mayanagi, Mingyue Jin, Kazuhiro Aoyama, Takuo Yasunaga

Cytoskeleton ( Wiley ) 73 ( 7 ) 365 - 374 2016年06月

Evaluation of a 2k CCD camera with an epitaxially grown CsI scintillator for recording energy-filtered electron cryo-micrographs 査読有り

YASUNAGA Takuo, WAKABAYASHI Takeyuki

Journal of electron microscopy 57 ( 3 ) 101 - 112 2008年06月

Atomic model construction of protein complexes from electron micrographs and visualization of their 3D structure using a virtual reality system 査読有り国際誌

Noda K., Nakamura M., Nishida R., Yoneda Y., Yamaguchi Y., Tamura Y., Nakamura H., Yasunaga T.

Journal of Plasma Physics 72 ( 6 ) 1037 - 1040 2006年12月

担当区分：最終著者,　責任著者記述言語：英語掲載種別：研究論文（学術雑誌）

The methods and applications that integrate electron microscopic density maps and comparative atomic coordinates to generate atomic models of protein complexes and their assemblies have recently advanced. Here, we also report on a newly developed tool for integration between density maps at a spatial resolution of about one nanometer and atomic coordinates by introducing the spatial constraints into a molecular dynamics calculation, which we call spatially restricted molecular dynamics. We, successfully, constructed the atomic models well-fitted to the density maps generated from nine different atomic coordinates of proteins. The method will give us the useful, refined, and presumable atomic structure of macromolecules to elucidate the relationship between their structure and functions. © 2006 Cambridge University Press.

DOI： 10.1017/S0022377806005174

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計測分析を未来につなぐためのデータの在り方と標準化招待有り

安永卓生

計測標準と計量管理 ( （一社）日本計量振興協会 ) 73 ( 4 ) 4 - 12 2024年02月

高等学校の探究科目／情報科目におけるシミュレーションの位置づけに関する一考査読有り

安永卓生

シミュレーション ( 日本シミュレーション学会 ) 42 ( 3 ) 188 - 193 2023年09月

計測分析機器の出力データフォーマット共通化査読有り

一村信吾, 重藤知夫, 安永卓生, 井上信介

応用物理 92 ( 3 ) 142 - 146 2023年03月

A percentile rank score of group productivity: an evaluation of publication productivity for researchers from various fields 査読有り国際誌

Yamamoto K., Yasunaga T.

Scientometrics 127 ( 4 ) 1737 - 1754 2022年04月

担当区分：最終著者記述言語：英語掲載種別：研究論文（学術雑誌）

The difficulty in evaluating the research performance of groups is attributable to the following two factors: 1) difference of population size or discipline of group members and 2) skewed distribution of the research performance of individuals. This study attempts to overcome this difficulty, focusing on the research performance based on publication productivity. We employ the normalized index for the number of papers, in which publication efficiency was considered and disciplinary variation in the publication intensity was corrected by the disciplinary averages, to calculate a new percentile rank score. The score was developed on the basis of the principle that a person who is rare is valuable. The score was also tested with publication data for faculty members of 17 Japanese universities. The employment of the normalized index increased the score of universities with relatively few faculty members working in the disciplines of high productivity, resulting in more plausible university rankings. The rankings show a high correlation with those for a previously established percentile rank score, which was developed for citation analysis, and they are consistent with the judgment by evaluators of several universities under study. The advantage of the new score over the previous one is that it has no room for arbitrariness in determining the scheme of rank classification and the weights given to each rank class.

DOI： 10.1007/s11192-022-04278-w

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巨大システムとしてのクライオ電子顕微鏡法の自動化から自働化への展開「（共著）」招待有り査読有り

安永卓生, 田中康太郎, 岩嵜彩夏, 塚本崇文, 本多康久

顕微鏡 ( 公益社団法人日本顕微鏡学会 ) 56 ( 1 ) 43 - 47 2021年04月

担当区分：筆頭著者記述言語：日本語掲載種別：記事・総説・解説・論説等（学術雑誌）

クライオ電子顕微鏡を利活用する時代が到来した．単粒子解析法は，原子レベルでの構造解析により構造生物学の柱となってきた．また，電子線トモグラフィー法は，細胞や組織における新しい描像を示しつつある．しかしSN比の低い画像であるが故に，多量の画像を必要とする．そのため，適切なUIに加え，自動撮影と画像処理システムと組み合わせ，画像の質を迅速に評価せねばならない．自動化から自働化へ，創発的な振る舞いが次の時代を興す．

DOI： 10.11410/kenbikyo.56.1_43

Kyutacar

その他リンク： http://hdl.handle.net/10228/00008831

九州工業大学における多面的・総合的な入試の制度設計検証――評価結果および「ジェネリック・スキル」等の比較からの一考察―― 査読有り

花堂奈緒子，播磨良輔，安永卓生

大学入試研究ジャーナル 2021年03月

生物物理学を牽引する新技術査読有り

安藤敏夫, 伊藤隆, 杉田有治, 南後恵理子, 安永卓生, 岡田康志, 神田元紀

生物物理 ( 一般社団法人日本生物物理学会 ) 61 ( 2 ) 111 - 118 2021年01月

Conformational equilibrium of NADPH–cytochrome P450 oxidoreductase is essential for heme oxygenase reaction 査読有り

Sugishima M., Taira J., Sagara T., Nakao R., Sato H., Noguchi M., Fukuyama K., Yamamoto K., Yasunaga T., Sakamoto H.

Antioxidants 9 ( 8 ) 1 - 13 2020年08月

記述言語：英語掲載種別：研究論文（学術雑誌）

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Heme oxygenase (HO) catalyzes heme degradation using electrons supplied by NADPH–cytochrome P450 oxidoreductase (CPR). Electrons from NADPH flow first to FAD, then to FMN, and finally to the heme in the redox partner. Previous biophysical analyses suggest the presence of a dynamic equilibrium between the open and the closed forms of CPR. We previously demonstrated that the open-form stabilized CPR (∆TGEE) is tightly bound to heme–HO-1, whereas the reduction in heme–HO-1 coupled with ∆TGEE is considerably slow because the distance between FAD and FMN in ∆TGEE is inappropriate for electron transfer from FAD to FMN. Here, we characterized the enzymatic activity and the reduction kinetics of HO-1 using the closed-form stabilized CPR (147CC514). Additionally, we analyzed the interaction between 147CC514 and heme–HO-1 by analytical ultracentrifugation. The results indicate that the interaction between 147CC514 and heme–HO-1 is considerably weak, and the enzymatic activity of 147CC514 is markedly weaker than that of CPR. Further, using cryo-electron microscopy, we confirmed that the crystal structure of ∆TGEE in complex with heme–HO-1 is similar to the relatively low-resolution structure of CPR complexed with heme–HO-1 in solution. We conclude that the “open–close” transition of CPR is indispensable for electron transfer from CPR to heme–HO-1.

DOI： 10.3390/antiox9080673

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入学者選抜と各種評価法による伸びしろの分析査読有り

安永卓生，播磨良輔，藤江美奈，山下修充

大学入試研究ジャーナル 2020年03月

Molecular dynamics study on DNA damage by tritium disintegration 査読有り

Nakamura H., Miyanishi H., Yasunaga T., Fujiwara S., Mizuguchi T., Nakata A., Miyazaki T., Otsuka T., Kenmotsu T., Hatano Y., Saito S.

Japanese Journal of Applied Physics 59 ( SA ) 2020年01月

記述言語：英語掲載種別：研究論文（国際会議プロシーディングス）

© 2019 The Japan Society of Applied Physics. Using molecular dynamics (MD) simulation, we simulate the structural change of a telomeric DNA by β-decay of substituted tritium to helium-3. The configuration of the telomeric DNA is obtained by removing TRF2 protein from the TRF2-Dbd-DNA complex (Protein Data Bank ID is 3SJM). We assume that hydrogens (H) of guanines in the telomeric DNA are replaced to helium-3. Since this replacement of the H atoms to the 3He atoms changes the charge distribution significantly, the charge distribution used in the MD simulation for the modified guanine is obtained by the density functional theory calculations. We adopt, as the MD simulation, nanoscale molecular dynamics code with CHARMM36 force field using Langevin thermostat and Nosé-Hoover Langevin piston to control the temperature and pressure of the system, respectively. Moreover, changing both the number of replaced guanine N and the temperature of the system T, we calculate the root mean square deviation RMSD to quantify the dependence of the durability of the telomeric DNA on the β-decays. From the MD simulation, it is found that as N or T becomes larger, the RMSD of the DNA becomes also larger. Namely, it denotes that as the intensity of the β-decays becomes larger or as the temperature is increased, the DNA structure becomes more fragile.

DOI： 10.7567/1347-4065/ab460d

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顕微鏡学における新たな鏡としての機械学習招待有り査読有り

安永卓生

顕微鏡 ( 公益社団法人日本顕微鏡学会 ) 55 ( 3 ) 103 - 103 2020年01月

難加工研磨におけるフラーレン結合型機能性ナノ微粒子に関する研究査読有り

久吉楓也, 鈴木恵友, Tsai Yueh-Hsun, Khajornrungruang Panart, 安永卓生, 高崎寛子, 大内将吉

精密工学会学術講演会講演論文集 ( 公益社団法人精密工学会 ) 2020 ( 0 ) 486 - 487 2020年01月

記述言語：日本語掲載種別：研究論文（研究会，シンポジウム資料等）

本研究では粒径が数十nm〜百nm程度の粒子径を持つダイヤモンドなどコア粒子上にフラーレン分子を吸着させ，紫外線照射のほかに，マイクロ波合成法を併用させることでフラーレンを新規炭素同素体へ物質変換を行い，研磨微粒子上に安定化した数nmレベルの機能性炭素層を形成する．ここでは形成された新規炭素同素体の分類を行うとともに難加工基板に対する研磨性能の影響について評価する．

DOI： 10.11522/pscjspe.2020S.0_486

その他リンク： https://ci.nii.ac.jp/naid/130007896718

単粒子解析におけるタンパク質構造分類のための深層学習アプローチの動向招待有り査読有り

馬水信弥, 田中康太郎, 安永卓生

顕微鏡 ( 公益社団法人日本顕微鏡学会 ) 55 ( 3 ) 104 - 108 2020年01月

担当区分：責任著者記述言語：日本語掲載種別：記事・総説・解説・論説等（学術雑誌）

クライオ電子顕微鏡による単粒子解析では，試料中に含まれる複数のタンパク質構造を分類しながら解くことが出来る．ただし分類された構造間のダイナミクスの情報は類推するしかない．この問題について2020年に発表された三次元再構成およびクラス分類を行うための深層学習アプローチであるcryoDRGNは，離散的なデータ分割による構造分類を脱却し，連続的な構造分類を実現した．そこでは，オートエンコーダーをベースとし，入力粒子画像から投影パラメーターに依存する情報を分離して潜在空間を構築している．本稿では従来の構造分類と，cryoDRGNおよびその背景となる深層学習のトピックについて解説を行ったのち，構造分類のベンチマークとして6種類の複合体を有するGroEL/ESの実データについて三次元再構成とその分類を試みた．

DOI： 10.11410/kenbikyo.55.3_104

Kyutacar

その他リンク： https://ci.nii.ac.jp/naid/130007967723

Molecular dynamics study on DNA damage by tritium disintegration 査読有り

Hiroaki Nakamura1,2, Hisanori Miyanishi2, Takuo Yasunaga3, Susumu Fujiwara4, Tomoko Mizuguchi4, Ayako Nakata5, Tsuyoshi Miyazaki5, Takao Otsuka6, Takahiro Kenmotsu7, Yuji Hatano8 and Shinji Saito

Japanese Journal of Applied Physics 59 2019年11月

Structural Changes in Tritium-Substituted Polymeric Materials by Beta Decays: A Molecular Dynamics Study 査読有り国際誌

LI Haolun, FUJIWARA Susumu, NAKAMURA Hiroaki, MIZUGUCHI Tomoko, YASUNAGA Takuo, OTSUKA Takao, KENMOTSU Takahiro, HATANO Yuji, SAITO Shinji

Plasma and Fusion Research ( 一般社団法人プラズマ・核融合学会 ) 14 ( 0 ) 3401106 - 3401106 2019年08月

記述言語：英語掲載種別：研究論文（学術雑誌）

The molecular mechanism through which how beta decays in tritium-substituted species damage DNA and polymeric materials is still unknown. Molecular dynamics simulations of hydrogen-removed polyethylene were performed to predict the structural change of the polyethylene chain after the substituted tritium decays. We calculated the potential energy, the global orientational order parameter, and the average number of consecutive trans bonds. The results are that, the greater the number of removed hydrogen atoms, the higher the potential energy and the lower the value of the global orientational order parameter and the average number of consecutive trans bonds. Thus, after losing hydrogen, polyethylene becomes poorer in terms of both thermal and structural stabilities.

DOI： 10.1585/pfr.14.3401106